Redetermination of germacrone type II based on single-crystal X-ray data

The crystal structure model of germacrone type II determined from single-crystal X-ray data is compared with that of a previous synchrotron X-ray powder study

The extraction and purification procedures, crystallization and crystal structure refinement (single-crystal X-ray data) of germacrone type II, C 15 H 22 O, are presented.The structural results are compared with a previous powder X-ray synchrotron study [Kaduk et al. (2022).Powder Diffr.37, 98-104], revealing significant improvements in terms of accuracy and precision.Hirshfeld atom refinement (HAR), as well as Hirshfeld surface analysis, give insight into the intermolecular interactions of germacrone type II.
We confirm that (1) crystallizes in the monoclinic space group C2/c.The unit-cell volume of 2579.78 (10) A ˚3 at a temperature of 100 K is about 4% smaller than that of 2684.06 (4) A ˚3 determined at room temperature.Fig. 1 shows the molecular structure of (1) and Fig. 2 the packing of the molecules along the crystallographic b direction.The most prominent feature with respect to the crystal packing aspects of (1) is the carbonyl group (C1 O1) next to the C CMe 2 entity [C2 C13(C14H 3 )(C15H 3 )].A Hirshfeld surface analysis using CrystalExplorer (Spackman et al., 2021) reveals that the carbonyl group is responsible for the only contacts of (1) with its periodic environment, with distances below the sum of the van der Waals radii (Fig. 3, red contacts).Numerical details of the contacts involving H atoms below 5 A ˚are listed in Table 1.In comparison with the room-temperature powder study, we found longer hydrogen-acceptor (H� � �A) distances, e.g. with one of the shortest H� � �A contacts being 2.59 (1) A ˚, while it was reported at 2.473 A ˚by Kaduk et al. (2022).A possible reason for this difference may be that we refined C-H distances directly based on the single-crystal X-ray diffraction data, employing Hirshfeld Atom Refinement (HAR).It has been reported that HAR yields C-H bond lengths that are as accurate as neutron data (Woin ´ska et al., 2016), so we are confident that these distances for germacrone type II are improved compared to the previous powder study.
In Table 2, the bond lengths between all atoms heavier than hydrogen are compared between the current single-crystal X-ray study and the previous powder study by Kaduk et al. (2022).The accuracy of the bond lengths differs by an entire order of magnitude and some distances differ strongly.For example, the C5-C12 bond to the methyl group of C12 is heavily underestimated [1.395 (12) A ˚] compared to 1.5017 (10) A ˚determined in the current study.The higher accuracy and precision of the current model results from the single-crystal X-ray data and the use of a successful nonspherical description of the atoms, but also from the lowtemperature data.The overlap of both molecular structures (Fig. 4) underlines the difference between the two structure refinements.
However, the Hirshfeld surface analysis (Fig. 3) is in close agreement with the results by Kaduk et al. (2022).The inter-molecular interaction in germacrone type II is of primarily dispersion character of H� � �H contacts (81.1%), with the remainder mostly consisting of O� � �H contacts (9.5%) and O� � �C contacts (0.8%).
Table 2 Comparison of bond lengths (A ˚) determined from the current singlecrystal X-ray study and from the powder study by Kaduk et al. (2022).Note: (*) atom labels were adopted from the current single-crystal X-ray study for better comparison.

Figure 1
The molecular structure of (1) with the atomic labelling scheme.Anisotropic displacement ellipsoids are drawn at the 50% probability level.Bond lengths (A ˚), except for C(sp 3 )-C(sp 3 ) and C(sp 2 )-C(sp 2 ) bonds, are indicated.

Figure 2
Crystal packing of (1) along the crystallographic b direction.Anisotropic displacement ellipsoids are drawn at the 50% probability level.

Synthesis and crystallization
The essential oil (EO) from the leaves of Geranium macrorrhizum L. was obtained by steam distillation, using a conventional distillation vessel with a capacity of 2.5 m 3 .The target terpenoid was isolated from the resulting EO.For this purpose, approximately 1.0 g of EO was dissolved in 5.0 ml of 99% vol.ethanol.To this solution, distilled water was subsequently added dropwise until a faint opalescence appeared.The homogeneity of the latter was restored by adding 200 ml of ethanol.The resulting solution was allowed to stand in a refrigerator for several hours.The crystals formed were separated from the remaining solution and purified twice by the same methodology.Approximately 200 mg of thin acicular crystals were thus obtained.

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 3. Refinement of the initial structure solution as determined by SHELXT (Sheldrick, 2015) was performed using olex2.refine(Dolomanov et al., 2009;Bourhis et al., 2015).The refined structure was used as an input to perform an iterative Hirshfeld atom refinement (HAR) using NoSpherA2 (Kleemiss et al., 2021) at the R2SCAN/cc-pVDZ level of theory until convergence was reached after eight cycles.This allowed us to model all atoms, including H atoms anisotropically without any constraints or restraints on the structural model.
Meurer et al. � C 15 H 22 O IUCrData (2024).9, x240346 Figure 4Overlayed molecular structures of germacrone type II determined in this work (ellipsoids connected by orange bonds) and from previous powder data(Kaduk et al., 2022; blue spheres).Ellipsoids and spheres are drawn at the 50% probability level.

Table 3
Experimental details.